They get shelved together and described with the same three words — fermented soya products — which makes them sound like variations on a theme. They aren't. A jar of miso and a block of tempeh have about as much in common as bread and beer: same raw material, entirely different outcome.
The one distinction that explains most of it
Two questions sort these foods almost completely.
What's doing the fermenting? Some are made by moulds. One is made by a bacterium. That's not a technicality; it changes the flavour, the texture and the timescale.
Does the bean survive? In some, the bean is still recognisably a bean at the end. In others it's been dismantled into a paste or a liquid.
Koji
Made by: Aspergillus oryzae, a mould What it is: not a finished food
Koji is the odd one out, because you don't really eat it on its own. It's steamed rice or barley — sometimes soya — inoculated with A. oryzae and left in a warm room until the grains are furred with white mould.
What you've made is an enzyme factory. The mould floods the grain with amylases and proteases that break starch into sugar and protein into amino acids. Koji is then the starting ingredient for other things: miso, soy sauce, sake, mirin.
Miso
Made by: koji mould, plus salt and time Bean status: dismantled
Cooked soya beans are mashed with koji and salt and left to age — months for a pale, sweet shiro miso, years for a dark, aggressive one. The koji enzymes work through the beans, and the salt keeps everything else out.
The result is a paste. There's no bean left to speak of, which is the point: what you get is concentrated savouriness, the amino acids the mould liberated from the protein. It dissolves into stock, thins into a dressing, works as a marinade.
Soy sauce
Made by: koji mould, then brine Bean status: dissolved entirely
Soya beans and roasted wheat are inoculated with koji, then submerged in salt brine and left to ferment for months. The liquid is pressed off at the end.
Same organism as miso, same starting bean, different geometry — miso keeps everything in the pot, soy sauce strains the solids out and keeps the liquid. Worth knowing that the wheat is not optional in most soy sauce, which matters if you're avoiding gluten.
Tempeh
Made by: Rhizopus, a mould Bean status: entirely intact
Whole cooked soya beans are inoculated with Rhizopus and held somewhere warm for a day or two. The mould grows through the gaps and binds the beans into a firm cake.
Nothing is dismantled. You can see the individual beans through the white mycelium, and the fibre is all still there. This is the crucial difference from miso and soy sauce — tempeh is still food you chew, not a seasoning. It's also the reason it works as a protein rather than a flavouring.
Indonesian rather than Japanese, which sets it apart from everything else on this list.
Natto
Made by: Bacillus subtilis, a bacterium Bean status: intact, but transformed
The outlier. Natto isn't made by a mould at all — cooked soya beans are fermented with Bacillus subtilis, and the bacterium produces long strands of polyglutamic acid that make the finished beans famously sticky and stringy. The smell is powerful and the texture is like nothing else in food.
It's also nutritionally remarkable in one specific way. Natto is by some distance the richest known food source of vitamin K2 in the menaquinone-7 form — one review puts it at roughly a hundred times the level found in most cheeses. If you've seen K2 supplements advertised, natto is usually where the raw material comes from.
The whole thing on one page
| Organism | Type | Bean | Origin | Use | |
|---|---|---|---|---|---|
| Koji | A. oryzae | Mould | Grain, not bean | Japan | Ingredient for other foods |
| Miso | A. oryzae | Mould | Paste | Japan | Seasoning |
| Soy sauce | A. oryzae | Mould | Liquid | China, then Japan | Seasoning |
| Tempeh | Rhizopus | Mould | Whole, bound | Indonesia | Main ingredient |
| Natto | B. subtilis | Bacterium | Whole, sticky | Japan | Eaten as is |
Four of these rely on mould fermentation somewhere in the process, while natto relies on a bacterium. Two foods you eat as food, three you use to season other things.
Where to start
If you've never eaten any of them, start with tempeh. It's the least alarming — firm, nutty, closer to a savoury cake than anything else here — and it behaves predictably in a pan. It's also the only one that works as the substantial part of a meal.
Miso is the easiest to keep in the fridge and the hardest to use badly. Soy sauce you already own.
Natto is a project. Approach when ready. For what it's worth, we bake ours into a crisp, which is a rather less traditional destination than any of the above.
If you want the fuller picture on tempeh specifically, we've written about what it is, how it differs from tofu, and why it being a mould is less strange than it sounds.
Keep reading
- What Is Tempeh? A Simple Guide to Our Hero Ingredient
- Tempeh vs Tofu: What’s the Difference?
- What Does Fermentation Actually Do to Tempeh?
- Is Tempeh Gluten-Free? What to Check
- We Eat Mould Constantly. Why Does Tempeh Seem Different?
From tempeh to your snacking plate. Meet TEMPTÉ →
Sources
- Natto microbiology and menaquinone-7 content: Afzaal et al., Biochemistry Research International, 2022
- Bacillus subtilis var. natto and polyglutamate strand formation: Rocchi et al., Heliyon, 2024
- A. oryzae in koji-based fermentation: Dupont et al., Microbiology Spectrum
- Tempeh fermentation and Rhizopus: Tempeh and Fermentation, Applied Sciences, 2025